[GeneX-dev] Re: Questions about command line interface for loading "bulk" data

[<ja...@op...>]

Hrishikesh Deshmukh <hde...@gm...> writes:

> 1) I assume for the options exp,ad,dtdim, fe the primary keys are the
> accession numbers which are generated once we use the GUI to insert
> experiment, ad and qt-dim?!

Yes, correct. If this isn't clear in the documentation for the script,
let me know, and suggest some wording as to how to improve it, and I
will be happy to make it more clear.

> 2) Since for Affy we load CDF and thats our AD as well, so i just take
> the accession number from the CDF table (there is none in the browsing
> interface).

CDF files are just Affy's way of specifying an ArrayDesign. So there
is no 'CDF' table, it is entered into the ArrayDesign table.

> 3) Correct me on this one: I have to use GUI to insert exp, ad and
> qt-dim, fe  and then use command line interface to load the "bulk"
> files?!!! Basically create the file as shown in the example with PBA
> and MBA......

Correct.

The FE SW must already be in the system - no one but a developer can
add new ones. After the trouble I had explaining the regexp based
system, I realized it was too complicated. So now, all the information
is hard coded in the file parsing system.

I am still (slowly) working on the generic tool to enable loading of
arbitrary files, and I have only one more step to complete and I can
fully test it, document it, and release it to you for more testing. 

Creating an Experiment is something that is done once for each, well,
experiment. So once it is created you can continue to load new data
into it as more hybridizations are completed in the lab.

The AD and QT Dim will only be loaded once, and then re-used again and
again.

Once these pieces are in the DB (using the GUI tools), then you can
use either the GUI loader to load multiple files (more work I believe)
or the command line tool together with the load file (less work when
there are many arrays to load - I believe).

> Sorry the last question sounds really stupid but i want to make sure
> that the workflow part can be smoothed out incase there is any need
> and the same questions can go in the FAQ/docs.

No problems!

Happy New Year (from Chennai),
jas.